title: Faecal microbiota profile of Crohn's disease determined by terminal restriction fragment length polymorphism analysis.
abstract: BACKGROUND
  Terminal restriction fragment length polymorphism (T-RFLP) analyses are powerful tools to assess the diversity of complex microbiota. T-RFLPs permit rapid comparisons of microbiota from many samples.
  
  
  OBJECTIVE
  To perform T-RFLP analyses of faecal microbiota in Crohn's disease (CD) patients to investigate potential alterations in faecal microbial communities and furthermore to analyse the effects of elemental diet on faecal microbiota profiles.
  
  
  METHODS
  Thirty-four patients with CD and 30 healthy individuals were enrolled in the study. DNA was extracted from stool samples and 16S rRNA genes were amplified by PCR. PCR products were digested with BslI restriction enzymes and T-RF lengths were determined.
  
  
  RESULTS
  Faecal microbial communities were classified into seven clusters. Almost all healthy individuals (28/30) were included in cluster I, II and III, but the majority of CD patients (25/34) could be divided into another four clusters (cluster IV-VII). Prediction of bacteria based on the BslI-digested T-RFLP database showed a significant decrease in Clostridium cluster IV, Clostridium cluster XI and subcluster XIVa in CD patients. In contrast, Bacteroides significantly increased in CD patients. Significant increases in Enterobacteriales were also observed in CD patients. Furthermore, elemental diets modulated faecal bacterial communities in CD patients.
  
  
  CONCLUSIONS
  Terminal restriction fragment length polymorphism analyses showed that the diversity of faecal microbiota in patients with CD differed from that of healthy individuals. Furthermore, elemental diets modulated faecal microbiota composition, and this effect may be involved in mechanisms of clinical effects of elemental diet.
authors.affiliation: Department of Medicine, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Japan. andoh@belle.shiga-med.ac.jp
authors.forename: A
authors.initials: A
authors.lastname: Andoh
authors.forename: T
authors.initials: T
authors.lastname: Tsujikawa
authors.forename: M
authors.initials: M
authors.lastname: Sasaki
authors.forename: K
authors.initials: K
authors.lastname: Mitsuyama
authors.forename: Y
authors.initials: Y
authors.lastname: Suzuki
authors.forename: T
authors.initials: T
authors.lastname: Matsui
authors.forename: T
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Y
authors.initials: Y
authors.lastname: Benno
authors.forename: Y
authors.initials: Y
authors.lastname: Fujiyama
mesh_terms: D000328:Adult; D019540:Area Under Curve; D016022:Case-Control Studies; D003424:Crohn Disease / Q000382:microbiology*; D004269:DNA, Bacterial / Q000032:analysis*; D005243:Feces / Q000382:microbiology*; D005260:Female; D006801:Humans; D008297:Male; D054892:Metagenome / Q000235:genetics*; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA / Q000379:methods*; D055815:Young Adult
chemical_list: D004269:DNA, Bacterial